Phylogenetics and the origin of species

Phylogenetic relationships among cetaceans revealed by Y-chromosome sequences

The Y chromosome has recently come into the spotlight as a new and efficient genetic marker for tracing paternal lineages. We reconstructed cetacean phylogeny using a 1.7-kbp fragment of the non-recombining Y chromosome (NRY), including the SRY gene and a flanking non-coding region. The topology of the Y-chromosome tree is robust to various methods of analysis and exhibits high branch-support values, possibly due to the absence of recombination, small effective population size, and low homoplasy. The Y-chromosome tree indicates monophyly of each suborder, Mysticeti and Odontoceti, with high branch support values (BS> or =86%; PP> or =98%). In the Odontoceti clade, three superfamilies, Physeteroidea, Ziphioidea, and Delphinoidea, diverged soon after the split between Mysticeti and Odontoceti. Our analysis allows resolution of this rapid radiation and indicates that Physeteroidea is basal in the Odontoceti clade (BS, 99%; PP, 100%; MBS, 61%). The major split within the superfamily Delphinoidea is between the Delphinidae clade and the Monodontidae+ Phocoenidae clade. The phylogenetic relationships among delphinid species are ambiguous, probably because of the rapid radiation of this family. In the Mysticeti clade, the first major split is between Balaenidae and Balaenopteridae; within Balaenopteridae, a Balaenoptera acutorostrata+B. bonaerensis (minke whales) clade forms a sister clade with the other balaenopterid species. Megaptera novaeangliae is nested within Balaenoptera, making the latter paraphyletic. The low homoplasy exhibited by the Y-chromosome data presented here suggests that an extended data set incorporating longer sequences would provide better resolution of cetacean lower-level pylogeny.

Species concepts and species delimitation

The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.

Does organismal pedigree impact the magnitude of topological congruence among gene trees for unlinked loci?

One of the fundamental assumptions in the multi-locus approach to phylogeographic studies is that unlinked loci have independent genealogies. For this reason, congruence among gene trees from unlinked loci is normally interpreted as support for the existence of external forces that may have concordantly shaped the topology of multiple gene trees. However, it is also important to address and quantify the possibility that gene trees within a given species are all inherently constrained to some degree by their shared organismal pedigree, and thus in this strict sense are not entirely independent. Here we demonstrate by computer simulations that gene trees from a shared pedigree tend to display higher topological concordance than do gene trees from independent pedigrees with the same demographic parameters, but we also show that these constraining effects are normally minor in comparison to the much higher degree of topological concordance that can routinely emerge from external phylogeographic shaping forces. The topology-constraining effect of a shared pedigree decreases as effective population size increases, and becomes almost negligible in a random mating population of more than 1,000 individuals. Moreover, statistical detection of the pedigree effect requires a relatively large number of unlinked loci that far exceed what is typically used in current phylogeographic studies. Thus, with the possible exception of extremely small populations, multiple unlinked genes within a pedigree can indeed be assumed, for most practical purposes, to have independent genealogical histories.

The origin and colonization history of the barley scald pathogen Rhynchosporium secalis

The origins of pathogens and their past and present migration patterns are often unknown. We used phylogenetic haplotype clustering in conjunction with model-based coalescent approaches to reconstruct the genetic history of the barley leaf pathogen Rhynchosporium secalis using the avirulence gene NIP1 and its flanking regions. Our results falsify the hypothesis that R. secalis emerged in association with its host during the domestication of barley 10,000 to 15,000 years ago in the Fertile Crescent and was introduced into Europe through the migration of Neolithic farmers. Estimates of time since most recent common ancestor (2500-5000 BP) placed the emergence of R. secalis clearly after the domestication of barley. We propose that modern populations of R. secalis originated in northern Europe following a host switch, most probably from a wild grass onto cultivated barley shortly after barley was introduced into northern Europe. R. secalis subsequently spread southwards into already established European barley-growing areas.

An evaluation of LSU rDNA D1-D2 sequences for their use in species identification

Background

Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region.

Results

Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800–1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (<< 0.1% on average) indicating that concerted evolution is very effective in most cases. Studies in two fish taxa (genus Cottus and genus Aphyosemion) show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus) that this is indeed possible.

Conclusion

The D1-D2 LSU region is a suitable marker region for applications in DNA based species identification and should be considered to be routinely used as a marker complementing broad scale studies based on mitochondrial markers.

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi

The claim that eukaryotic micro-organisms have global geographic ranges, constituting a significant departure from the situation with macro-organisms, has been supported by studies of morphological species from protistan kingdoms. Here, we examine this claim by reviewing examples from another kingdom of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon the method of species recognition. While some fungal species defined by morphology show global geographic ranges, when fungal species are defined by phylogenetic species recognition they are typically shown to harbour several to many endemic species. We advance two non-exclusive reasons to explain the perceived difference between the size of geographic ranges of microscopic and macroscopic eukaryotic species when morphological methods of species recognition are used. These reasons are that microbial organisms generally have fewer morphological characters, and that the rate of morphological change will be slower for organisms with less elaborate development and fewer cells. Both of these reasons result in fewer discriminatory morphological differences between recently diverged lineages. The rate of genetic change, moreover, is similar for both large and small organisms, which helps to explain why phylogenetic species of large and small organisms show a more similar distribution of geographic ranges. As a consequence of the different rates in fungi of genetic and morphological changes, genetic isolation precedes a recognizable morphological change. The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change.

DNA Barcoding Will Often Fail to Discover New Animal Species over Broad Parameter Space

With increasing force, genetic divergence of mitochondrial DNA (mtDNA) is being argued as the primary tool for discovery of animal species. Two thresholds of single-gene divergence have been proposed: reciprocal monophyly, and 10 times greater genetic divergence between than within species (the "10x rule"). To explore quantitatively the utility of each approach, we couple neutral coalescent theory and the classical Bateson-Dobzhansky-Muller (BDM) model of speciation. The joint stochastic dynamics of these two processes demonstrate that both thresholds fail to "discover" many reproductively isolated lineages under a single incompatibility BDM model, especially when BDM loci have been subject to divergent selection. Only when populations have been isolated for > 4 million generations did these thresholds achieve error rates of < 10% under our model that incorporates variable population sizes. The high error rate evident in simulations is corroborated with six empirical data sets. These properties suggest that single-gene, high-throughput approaches to discovering new animal species will bias large-scale biodiversity surveys, particularly toward missing reproductively isolated lineages that have emerged by divergent selection or other mechanisms that accelerate reproductive isolation. Because single-gene thresholds for species discovery can result in substantial error at recent divergence times, they will misrepresent the correspondence between recently isolated populations and reproductively isolated lineages (= species).

Multiple gene genealogies and AFLPs suggest cryptic speciation and long-distance dispersal in the basidiomycete Serpula himantioides (Boletales)

Serpula himantioides (Boletales, Basidiomycota) produces thin resupinate basidiocarps on dead coniferous wood worldwide and causes damage in buildings as well. In this study, we present evidence for the existence of at least three phylogenetically defined cryptic species (referred to as Sib I-III) within the morphospecies S. himantioides, a conclusion based on analyses of sequence data from four DNA regions and amplified fragment length polymorphisms (AFLPS). A low degree of shared sequence polymorphisms was observed among the three lineages indicating a long-lasting separation. The AFLPs revealed two additional subgroups within Sib III. Results from mating studies were consistent with the molecular data. In Sib III, no correspondence between genetic and geographical distance was observed among isolates worldwide, presumably reflecting recent dispersal events. Our results indicate that at least two of the lineages (Sib II and Sib III) have wide sympatric distributions. A population genetic analysis of Sib III isolates, scoring sequence polymorphisms as codominant SNP markers, indicates that panmictic conditions exist in the Sib III group. This study supports the view that cryptic speciation is a common phenomenon in basidiomycete fungi and that phylogenetic species recognition can be a powerful inference to detect cryptic species. Furthermore, this study shows that AFLP data are a valuable supplement to DNA sequence data in that they may detect a finer level of genetic variation.

Migration, isolation, and speciation of hydrothermal vent limpets (Gastropoda; Lepetodrilidae) across the Blanco Transform Fault

The Sovanco Fracture Zone and Blanco Transform Fault separate the Explorer, Juan de Fuca, and Gorda ridge systems of the northeastern Pacific Ocean. To test whether such offsets in the ridge axis create barriers to along-axis dispersal of the endemic hydrothermal vent animals, we examined the genetic structure of limpet populations previously identified as Lepetodrilus fucensis McLean, 1988 (Gastropoda, Lepetodrilidae). Mitochondrial DNA sequences and patterns of allozyme variation revealed no evidence that the 150-km-long Sovanco Fracture Zone impeded gene flow between the Explorer and Juan de Fuca populations. In contrast, the 450-km-long Blanco Transform Fault separates the limpets into highly divergent northern and southern lineages that we recognize as distinct species. We describe southern populations from the Gorda Ridge (Seacliff) and Escanaba Trough as Lepetodrilus gordensis new species and refer northern populations from the Explorer and Juan de Fuca ridge systems to L. fucensis sensu stricto. The species are similar morphologically, but L. gordensis lacks a sensory neck papilla and has a more tightly coiled teleconch. To assess the degree of isolation between these closely related species, we used the Isolation with Migration method to estimate the time of population splitting, effective sizes of the ancestral and derived populations, and rates of migration across the Blanco Transform Fault.

Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies

Paracoccidioides brasiliensis is the etiologic agent of paracoccidioidomycosis, a disease confined to Latin America and of marked importance in the endemic areas due to its frequency and severity. This species is considered to be clonal according to mycological criteria and has been shown to vary in virulence. To characterize natural genetic variation and reproductive mode in this fungus, we analyzed P. brasiliensis phylogenetically in search of cryptic species and possible recombination using concordance and nondiscordance of gene genealogies with respect to phylogenies of eight regions in five nuclear loci. Our data indicate that this fungus consists of at least three distinct, previously unrecognized species: S1 (species 1 with 38 isolates), PS2 (phylogenetic species 2 with six isolates), and PS3 (phylogenetic species 3 with 21 isolates). Genealogies of four of the regions studied strongly supported the PS2 clade, composed of five Brazilian and one Venezuelan isolate. The second clade, PS3, composed solely of 21 Colombian isolates, was strongly supported by the alpha-tubulin genealogy. The remaining 38 individuals formed S1. Two of the three lineages of P. brasiliensis, S1 and PS2, are sympatric across their range, suggesting barriers to gene flow other than geographic isolation. Our study provides the first evidence for possible sexual reproduction in P. brasiliensis S1, but does not rule it out in the other two species.

Analysis of sex-linked sequences supports a new mammal species in Europe

European mammals have been the focus of particularly detailed taxonomic studies by traditional morphological methods. However, DNA analyses have the potential to reveal additional, cryptic species. We describe two highly divergent evolutionary lineages within a small Eurasian mammal, the field vole (Microtus agrestis). We show that the two lineages can be detected not only with maternally (mitochondrial DNA), but also with paternally (Y chromosome) and biparentally (X chromosome) inherited DNA sequences. Reciprocal monophyly of all genealogies and their congruent geographical distributions is consistent with reproductive isolation. Our results suggest that the field vole should be reclassified as two separate species.

Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees

Computer simulations were used to investigate population conditions under which phylogeographic breaks in gene genealogies can be interpreted with confidence to infer the existence and location of historical barriers to gene flow in continuously distributed, low-dispersal species. We generated collections of haplotypic gene trees under a variety of demographic scenarios and analyzed them with regard to salient genealogical breaks in their spatial patterns. In the first part of the analysis, we estimated the frequency in which the spatial location of the deepest phylogeographic break between successive pairs of populations along a linear habitat coincided with a spatial physical barrier to dispersal. Results confirm previous reports that individual gene trees can show 'haphazard' phylogeographic discontinuities even in the absence of historical barriers to gene flow. In the second part of the analysis, we assessed the probability that pairs of gene genealogies from a set of population samples agree upon the location of a geographical barrier. Our findings extend earlier reports by demonstrating that spatially concordant phylogeographic breaks across ;ndependent neutral loci normally emerge only in the presence of longstanding historical barriers to gene flow. Genealogical concordance across multiple loci thus becomes a deciding criterion by which to distinguish between stochastic and deterministic causation in accounting for phylogeographic discontinuities in continuously distributed species.

Adaptive speciation: the role of natural selection in mechanisms of geographic and non-geographic speciation

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate-namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive.

Mechanisms of fungal speciation

The objective of this review is to provide a synthesis of speciation theory, of what is known about mechanisms of speciation in fungi and from this, what is expected, and of ideas on how speciation can be elucidated in more fungal systems. The emphasis is on process rather than pattern. Phylogeographic studies in some groups, such as the agarics, demonstrate predominantly allopatric speciation, often through vicariance, as seen in many plants and animals. The variety of life history factors in fungi suggests, however, a diversity in speciation mechanisms that is borne out in comparison of some key examples. Life history features in fungi with a bearing on speciation include genetic mechanisms for intra- and interspecies interactions, haploidy as monokaryons, dikaryons, or coenocytes, distinctive types of propagules with distinctive modes of dispersal, as well as characteristic relationships to the substrate or host as specialized or generalist saprotrophs, parasites or mutualists with associated opportunities and selective pressures for hybridization. Approaches are proposed for both retrospective, phylogeographic determination of speciation mechanisms, and experimental studies with the potential for genomic applications, particularly in examining the relationship between adaptation and reproductive isolation.

The role of subspecies in obscuring avian biological diversity and misleading conservation policy

Subspecies are often used in ways that require their evolutionary independence, for example as proxies for units of conservation. Mitochondrial DNA sequence data reveal that 97% of continentally distributed avian subspecies lack the population genetic structure indicative of a distinct evolutionary unit. Subspecies considered threatened or endangered, some of which have been targets of expensive restoration efforts, also generally lack genetic distinctiveness. Although sequence data show that species include 1.9 historically significant units on average, these units are not reflected by current subspecies nomenclature. Yet, it is these unnamed units and not named subspecies that should play a major role in guiding conservation efforts and in identifying biological diversity. Thus, a massive reorganization of classifications is required so that the lowest ranks, be they species or subspecies, reflect evolutionary diversity. Until such reorganization is accomplished, the subspecies rank will continue to hinder progress in taxonomy, evolutionary studies and especially conservation.

Molecular and cytogenetic evidence for cryptic speciation within a rare endemic Malagasy lemur, the Northern Sportive Lemur (Lepilemur septentrionalis)

Evolutionary relationships of different populations of the threatened malagasy lemur Lepilemur septentrionalis were assessed by sequence analysis of mitochondrial DNA (D-loop region and partial Cyt b gene). One hundred and fifty nine samples were collected from five main different localities in the northern part of Madagascar. We applied the phylogenetic species concept based on fixed diagnostic differences to determine the status of different geographical populations. No nucleotide site diagnoses Ankarana from Andrafiamena or Analamera. However, numerous fixed differences separate Sahafary from all other populations. These results were corroborated by phylogenetic trees. As previous cytogenetic studies, our molecular data suggest that two cryptic species of Lepilemur occur in the extreme north of Madagascar. This speciation is probably caused by chromosomal rearrangements in at least one of the evolutionary lineages. Our study comprises another striking example of how molecular genetic assay can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. Our study indicates that the Sahafary population is a hitherto undescribed endangered endemic species which urgently needs conservation efforts.

AFLPs RESOLVE PHYLOGENY AND REVEAL MITOCHONDRIAL INTROGRESSION WITHIN A SPECIES FLOCK OF AFRICAN ELECTRIC FISH (MORMYROIDEA: TELEOSTEI)

Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.

Interspecific hybridization in plant‐associated fungi and oomycetes: a review

Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.

Evolution of drug resistance in Candida albicans

The widespread deployment of antimicrobial agents in medicine and agriculture is nearly always followed by the evolution of resistance to these agents in the pathogen. With the limited availability of antifungal drugs and the increasing incidence of opportunistic fungal infections, the emergence of drug resistance in fungal pathogens poses a serious public health concern. Antifungal drug resistance has been studied most extensively with the yeast Candida albicans owing to its importance as an opportunistic pathogen and its experimental tractability relative to other medically important fungal pathogens. The emergence of antifungal drug resistance is an evolutionary process that proceeds on temporal, spatial, and genomic scales. This process can be observed through epidemiological studies of patients and through population-genetic studies of pathogen populations. Population-genetic studies rely on sampling of the pathogen in patient populations, serial isolations of the pathogen from individual patients, or experimental evolution of the pathogen in nutrient media or in animal models. Predicting the evolution of drug resistance is fundamental to prolonging the efficacy of existing drugs and to strategically developing and deploying novel drugs.

Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents

Deep-sea hydrothermal vent species are widely dispersed among habitat islands found along the global mid-ocean ridge system. We examine factors that affect population structure, gene flow and isolation in vent-endemic mussels of the genus Bathymodiolus from the eastern Pacific Ocean. Mussels were sampled from localities including the Galapagos Rift (GAR, 0 degrees 48' N; 86 degrees 10' W) and the East Pacific Rise (EPR, 13 degrees N to 32 degrees S latitude) across a maximum distance of 4900 km. The sampled range crossed a series of topographical features that interrupt linear aspects of the ridge system, and it encompassed regions of strong cross-axis currents that could impede along-axis dispersal of mussel larvae. Examinations of mitochondrial DNA sequences and allozyme variation revealed significant barriers to gene flow along the ridge axis. All populations from the GAR and EPR from 13 degrees N to 11 degrees S were homogeneous genetically and appeared to experience unimpeded high levels of interpopulational gene flow. In contrast, mussels from north and south of the Easter Microplate were highly divergent (4.4%), possibly comprising sister-species that diverged after formation of the microplate approximately 4.5 Ma. Strong cross-axis currents associated with inflated bathymetry of the microplate region may reinforce isolation across this region.

Atherina punctata and Atherina lagunae (Pisces, Atherinidae), new species found in the Mediterranean sea. 2. Molecular investigations of three Atherinid species

On the basis of morphoanatomical parameters, the sand smelt species (Atherina boyeri Risso, 1810) is viewed as a highly polymorphic complex. In this study, intraspecific sequence variation in a portion of the cytochrome b gene was examined in 88 individuals from Tunisia and France. The correlation between the results of statistical analysis of the sequence data using a variety of tree-building algorithms and morphoanatomical analyses demonstrated the subdivision into three putative species: A. boyeri, which only includes non-punctuated fishes, A. punctata, which corresponds to punctuated fishes and A. lagunae, which corresponds to atherines living in lagoons.

The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout

Technical and biological hurdles have precluded the retrieval of nuclear gene genealogies within most species. Among these obstacles, the possibility of intragenic recombination is one of the most demanding challenges. We studied the utility of nuclear genes for intraspecific evolutionary inferences by selecting a nuclear gene that exhibits patterns of considerable geographic differentiation in the brown trout (Salmo trutta) species complex. Haplotype variation from a nucleotide sequence of approximately 3.7 kb encompassing a portion of the transferrin (TF) gene was surveyed in 31 brown trout individuals collected across the native Eurasian range. Statistically significant recombination and gene conversion events were detected. However, we showed that the substantial cladistic structure was not disrupted by recombination or gene conversion events and the additional structure was estimated to have emerged after those events. Because loci with unusually high levels of variation might indicate the presence of selection, we tested the hypothesis of neutrality and found some evidence for directional selection. The strong geographic signal observed in the TF genealogy, coupled with the current spatial distribution of electromorphs, gave us the ability to draw empirical phylogeographic inferences. We delineated the composition of current brown trout populations on the basis of 3,625 individuals electrophoretically scored for the TF locus. We hypothesized scenarios of historical radiation and dispersal events, thus providing new insights refining previous allozyme and mtDNA inferences. We infer that the most ancestral brown trout populations inhabited tributaries from the Black, Caspian, and Aral Sea drainages. An early radiation of the species occurred throughout the Mediterranean, followed by independent dispersal events from the Adriatic to the southernmost Iberian Atlantic and, more recently, a rapid expansion throughout most of the Atlantic drainages.

Genetic subdivision and biogeography of the Danubian rheophilic barb Barbus petenyi inferred from phylogenetic analysis of mitochondrial DNA variation

The barb Barbus petenyi is a cyprinid widely distributed throughout the mountain regions in the Danube River basin. Phylogenetic analysis of the DNA sequence variation at the mitochondrial cytochrome b gene over much of this range yielded three deep-branching (5.9-9.4% average divergence), well-supported haplotype clades with mutually exclusive geographic distributions and divergence times estimated to be in the Tertiary. The clades did not form an altogether monophyletic group as the most divergent one coalesced more recently with haplotypes of phylogenetically close species than with the other B. petenyi haplotypes. This pattern was supported by bootstrap and log-likelihood Shimodaira-Hasegawa tests. The other two were sister clades, but their distinctiveness was supported by previous allozyme data. Hence, from a taxonomic point of view, the current recognition of B. petenyi is erroneous, as it does not represent a single evolutionary lineage, and we suggest that three species be recognized instead. Substantial phylogeographic differences were evident among the three putative species, the two more southerly ones displaying significant structure, which suggested that they each survived in several glacial refugia throughout the Pleistocene. The phylogeographic pattern of multiple populations of rheophilic barbs with a history of long-term persistence and separation within the Danube River basin is novel within fishes and provides a hypothesis against which phylogeographic patterns among other similarly distributed rheophilic species may be compared.

Fine-level mycorrhizal specificity in the Monotropoideae (Ericaceae): specificity for fungal species groups

The Monotropoideae (Ericaceae) are non-photosynthetic angiosperms that obtain fixed carbon from basidiomycete ectomycorrhizal fungi. In previous work, we showed that each plant species is associated with a single genus or a set of closely related genera of ectomycorrhizal fungi. Here we show that the level of specificity is much higher. We used a molecular phylogenetic approach to contrast specificity patterns among eight plant lineages and three fungal genera. We relied on fungal nuclear internal transcribed spacer (nrITS) sequence data obtained from 161 basidiocarps and 85 monotropoid roots representing 286 sampled plants screened using restriction length polymorphisms. From the phylogenetic placement of fungal symbionts in fungal phylograms, we found that three basal (Sarcodes, Pterospora, Pleuricospora) and one derived lineage (Allotropa) of plants target narrow clades of closely related species groups of fungi, and four derived lineages (Monotropa hypopithys species group, Pityopus) target more distant species groups. Within most plant lineages, geography and photobiont association constrain specificity. Specificity extended further in Pterospora andromedea, in which sequence haplotypes at the plastid trn L-F region of 73 plants were significantly associated with different fungal species groups even in sympatry. These results indicate that both the macro- and microevolution of the Monotropoideae are tightly coupled to their mycorrhizal symbionts.

Time to the most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration

We analyzed sequences from a 275-bp hypervariable region in the 5' end of the mitochondrial DNA control region in 190 common chaffinches (Fringilla coelebs) from 19 populations in Europe and North Africa, including new samples from Greece and Morocco. Coalescent techniques were applied to estimate the time to the most recent common ancestor (TMRCA) and divergence times of these populations. The first objective of this study was to infer the locations of refugia where chaffinches survived the last glacial episode, and this was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene. Although extant populations in Iberia, Corsica, Greece, and North Africa harbor haplotypes that are basal in a phylogenetic tree, this information alone cannot be used to infer that these localities served as refugia, because it is impossible to infer the ages of populations and their divergence times without also considering the population genetic processes of mutation, migration, and drift. Provided we assume the TMRCAs of populations are a reasonable estimate of a population's age, coalescent-based methods place resident populations in Iberia, Corsica, Greece, and North Africa during the time of the last glacial maximum, suggesting these regions served as refugia for the common chaffinch. The second objective was to determine when populations began diverging from each other and to use this as a baseline to estimate current levels of gene flow. Divergence time estimates suggest that European populations began diverging about 60,000 years before present. The relatively recent divergence of populations in North Africa, Italy, and Iberia may explain why classic migration estimates based on equilibrium assumptions are high for these populations. We compare these estimates with nonequilibrium-based estimates and show that the nonequilibrium estimates are consistently lower than the equilibrium estimates.

Phylogeny of bovine species based on AFLP fingerprinting

The Bovini species comprise both domestic and wild cattle species. Published phylogenies of this tribe based on mitochondrial DNA contain anomalies, while nuclear sequences show only low variation. We have used amplified fragment length polymorphism (AFLP) fingerprinting in order to detect variation in loci distributed over the nuclear genome. Computer-assisted scoring of electrophoretic fingerprinting patterns yielded 361 markers, which provided sufficient redundancy to suppress stochastic effects of intraspecies polymorphisms and length homoplasies (comigration of non-homologous fragments). Tree reconstructions reveal three clusters: African buffalo with water buffalo, ox with zebu, and bison with wisent. Similarity values suggest a clustering of gaur and banteng, but bifurcating clustering algorithms did not assign consistent positions to these species and yak. We propose that because of shared polymorphisms and reticulations, tree topologies are only partially adequate to represent the phylogeny of the Bovini. Principal-coordinate analysis positions zebu between a gaur/banteng cluster and taurine cattle. This correlates with the region of origin of these species and suggests that genomic distances between the cattle species have been influenced by genetic exchange between neighbouring ancestral populations.